BACKGROUND

Global contamination of soil and aquatic ecosystems by pharmaceutical and microbiological pollutants (such as antimicrobial-resistant microorganisms and/or pathogens) raises severe concerns about impacts on ecosystem health and repercussions on humans and animals. Preserving ecosystems from adverse ecotoxicological effects of pharmaceuticals and their transformation products, and limiting the environmental spread of antimicrobial resistance and pathogens is imperative to reach several UN Sustainable Development Goals as well as the European Green Deal, Water Framework Directive and Biodiversity Strategy for 2030. In this context, the main scientific objective of Pharm-ERA is to develop and implement innovative concepts, methods and strategies to improve the monitoring and assessment of the environmental effects and risks of pharmaceuticals, their transformation products, antimicrobial resistances and pathogens from terrestrial to aquatic environments. The ultimate goal is to provide scientific evidence and expertise to contribute to reducing the environmental spread and impact of these chemical and microbiological contaminants and to preserve microbial diversity and functions across the soil-water-sediment continuum.

DESCRIPTION OF THE PhD PROJECT

Attached living aquatic microbial communities, also known as biofilms are mainly composed of bacteria, microalgae and fungi and play an important role in biodiversity and functioning of aquatic ecosystems. They are constantly exposed to multiple stressors, including pharmaceuticals and climate-related stressors.
To address the Triple Planetary Crisis of pollution, climate change and biodiversity loss this PhD-project aims to analyse the interdependency of antibiotics exposure and heat waves on biofilms by using a multi-omics approach. The objectives of the thesis are:
1- to define molecular response traits of biofilms to antibiotics,
2- quantitatively link molecular responses to phenotypic functional responses and changes in community structure,
3- to define biodiversity-functional relationships based on response traits
4- to provide a workflow for ecologically robust molecular thresholds for regulation and management to protect periphyton biodiversity and functioning.
To this end, model ecosystems (microcosms) will be used to expose biofilm communities to selected antibiotics and apply a factorial design to assess the interactive effects of climate-related stressors and antibiotic exposure. In close co-operation with Zahra at INRAE (France) a range of multi-omics approaches (metabolomics in combination with other omics levels such as metatranscriptomics or metaproteomics) will be implemented to identify interacting metabolic pathways upon combined exposure. Bioinformatics and biostatistics workflows will then be applied to derive molecular sensitivity thresholds and causal relationships for comparison across biological scales.
To further root molecular responses to functional and biodiversity changes as well as community tolerance, community-structural analyses (Metabarcoding) and functional analysis (e.g. primary and bacterial production of the respective autotrophic and heterotrophic biofilm component) will be combined.